Data from: Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum

Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation has been important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analyzed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signaling molecules. This study provides insight into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was likely present in the last common ancestor of animals.

长链非编码RNA（long non-coding RNAs，lncRNAs）在动物发育过程中发挥关键调控作用，已有假说提出，基于RNA的基因调控对于动物发育复杂性的演化至关重要。然而，当前绝大多数关于lncRNA基因调控的研究均以模式动物为实验对象，对于非两侧对称动物（non-bilaterians）中此类基因调控机制的认知仍极为匮乏。为此，本研究对钙质海绵毛壶（Sycon ciliatum）全胚胎发育阶段的RNA测序（RNA-Seq）数据展开分析，在该物种中鉴定出数百种发育阶段特异性表达的基因间长链非编码RNA（intergenic lncRNAs，lincRNAs）。对筛选出的部分lincRNAs进行原位杂交（in situ hybridization）实验，结果显示其在胚胎发育过程中呈现动态的时空表达模式。超过600种lincRNAs是差异表达基因模块的核心组成部分，这些模块同时包含已知的发育调控基因，例如转录因子与信号分子。本研究揭示了动物演化史上最早出现的支系之一的非编码基因组库，同时暗示基于RNA的基因调控极有可能存在于动物的最近共同祖先之中。